Summary Two resources for free computing at UW-Madison offered by the Center for High Throughput Computing (CHTC): – BadgerCompute: badgercompute.wisc.edu/ for Jupyter-based interactive notebooks in R, Python, or Julia computer programming languages. – High Throughput Computing for large compute projects. Free account by filling-in a request account form. Free computing @ UW There was a …
Summary Workshop Series available on Campus on R and Python. (For more details see further below.) – UW Libraries – Steenbock Library Workshops – UW Data Science Hub / Software Carpentry – Social Science Computing Cooperative (SSCC) Steenbock Library Workshops See details on announcement page: Learn how to use Python and/or R programming languages for …
Summary Simpson’s paradox is a fascinating statistical phenomenon where the observed relationship between two variables can be reversed when the data is divided into subgroups. For biologists and biochemists, this means that the correlation between two biological variables might change direction when considering an additional categorical variable, such as a specific species or experimental condition. …
Summary ChatMol is a ChatGPT plugin that offers a Free chatlite version that does not require an API key. ChatMol ChatMol is a PyMOL plugin based on large language models, that provide a conversational interface (CUI) for molecular operation and computation. Current supported models include models from OpenAI (ChatGPT versions), Anthropic (Claude versions), DeepSeek, and …
Summary “Explore how David Baker, Demis Hassabis, and John Jumper won the 2024 Nobel Prize in Chemistry for their advances in computer-assisted protein design.” Video: How AI Cracked the Protein Folding Code and Won a Nobel Prize This 22min19 video provides a very good explanation of the origins of the research in protein structure, from …
Summary The NIH offers 2D bioart (bioart.niaid.nih.gov) with a public domain license, and collections of 3D models (3d.nih.gov) Free 2D Bio Art The National Institute of Allergy and Infectious Diseases (NIAID), one of the 27 Institutes and Centers of the National Institutes of Health (NIH), has released a series of sketch art that may prove …
Summary Run the ColabFold version of AlphaFold2 on your laptop (slow without GPU) or on a large Linux cluster. The full tutorial with scripts is located at ColabFold with HTCondor What is AlphaFold2 Excerpt from a previous post (Five ways to run AlphaFold) AlphaFold can accurately predict 3D models of protein structures by providing an …
Summary Workshop Series available on Campus on R and Python. (For more details see further below.) – Biochem – Social Science Computing Cooperative (SSCC) – UW Libraries – SSteenbock Library Workshops – Computational Biology, Ecology, & Evolution (ComBEE) Study Groups R and Python at Biochem R and Python “Clubs” were established in late 2022. The …
Summary We run a script to compute the distance between 2 atoms in a series of PDB files with identical molecules in different conformations and save the distance results into a plain text file. No GUI PyMOL In previous posts I explained how we can use PyMOL as a command-line tool from a Terminal when …
Summary The new Numpy 2.0 is not compatible with many other packages, as I discovered after many lost hours. The final Docker images can be downloaded from alleleanalyzer. NumPy in a Docker I was interested to implement a process involving Python packages from a paper published in 2019: “AlleleAnalyzer: a tool for personalized and allele-specific …